On 2/27/17 12:49 AM, RAHUL SURESH wrote:
I am explaining my issues regarding complex simulation. I have 200ns conformer(OPLS FF) I have generated my ligand gro and itp file.(Using topolgen1_1) I have edited my protein gro file and made it into complex file as per the tutorials. I have made changes to my topol.top file. Now in my command for em.mdp I am getting 19 errors stating "NO DEFAULT BOND TYPE, ANGLE TYPE, ETC." Can you guide me with this?
This means the atom type assignment makes reference to bonded parameters that don't exist. That means one of two things: (1) either the atom type assignment is incorrect, requiring manual correction (as the script warns you, as it makes a lot of assumptions and is therefore rather dumb sometimes) or (2) you simply have a molecule for which parameters do not exist, requiring manual parametrization. For OPLS-AA, this requires QM calculations to get things like equilibrium geometries, vibrational frequencies, and dihedral potential energy scans.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
